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uniprot_get_proteome

Read-only

Fetch a UniProt proteome by UP ID, returning organism taxonomy, protein and gene counts, BUSCO completeness, annotation score, and chromosome/contig breakdown.

Instructions

Fetch a UniProt proteome by UP ID (e.g. UP000005640 = human reference). Returns organism, taxonomy lineage, protein count, gene count, BUSCO completeness score, annotation score, and component breakdown (chromosomes / contigs).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
proteome_idYesUniProt proteome ID, e.g. 'UP000005640' (human reference). Always starts with 'UP'.
response_formatNo'markdown' (default) for a human-readable report with a provenance footer, or 'json' for a machine-parseable structured payload with the same data. Any other value is rejected.markdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint and openWorldHint; description adds specific return fields (organism, taxonomy, counts, etc.), providing useful context beyond annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences, front-loaded with main purpose, no unnecessary information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Lists return fields; output schema exists for detailed structure. Could mention error handling for invalid ID, but overall sufficient for a fetch tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Adds meaning for proteome_id with example and prefix note; response_format is already well-documented in schema. Schema coverage is 100%, so description adds moderate value.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states it fetches a UniProt proteome by UP ID with a specific example, distinguishing it from sibling tools like uniprot_get_entry or uniprot_search_proteomes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Implies usage via 'Fetch a UniProt proteome by UP ID', but does not explicitly state when to use versus alternatives or provide exclusion criteria.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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